Can I rotate part of the mesh while reserving topology?
Its actually simple :)

First select the edge loop you need to seperate with Alt+RMB as shown in the picture below.



Then select the other remaining edges by right clicking on them....

When you're done selecting just the plate press P
Then choose Separate by Selection

Now rotate it as you like....

Now is the tricky part....

I'm not sure how others do this, but I do it in this way...

suppose the uppermost cube is your plate and the lower one as your main ship...



Now we've separated these two in the previous step...
Now make them a single object by  Shift+RMB selecting each object, and then pressing  Ctrl+J ..... 



Now go to edit mode and go to vertex select mode... 
and press  B  to box select the plate from Orthographic View (Num 5) or a comfortable angle...

For yours it may be right side (Num 3)
then select all the edges to be joined....

In your case it's just two edge loops (Shift+Alt+RMB)....



Then press F to make faces between them...

Now, it mightn't be the best technique but I found it works for me...
Hope it helps :)